Merge pull request #145 from apeltzer/fix-picard

Fix picard memory issue

Author: apeltzer

CHANGELOG.md

@@ -6,6 +6,12 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ## [Unpublished / Dev Branch]
 
+### `Added`
+
+### `Fixed`
+* [#145](https://github.com/nf-core/eager/issues/145) - Added Picard Memory Handling [fix](https://github.com/nf-core/eager/issues/144)
+
+
 ## [2.0.5] - 2019-01-28
 
 ### `Added`

conf/base.config

@@ -31,7 +31,10 @@ process {
   withName:convertBam {
     cpus = { check_max(8 * task.attempt, 'cpus') }
   }
-  
+  withName:makeSeqDict {
+    memory = { check_max( 16.GB * task.attempt, 'memory' ) }
+  }
+
   withName:bwa {
     memory = { check_max( 16.GB * task.attempt, 'memory' ) }
     cpus = { check_max(8 * task.attempt, 'cpus') }

main.nf

@@ -488,7 +488,7 @@ process makeSeqDict {
     mkdir -p seq_dict
     mv $fasta "seq_dict/${base}"
     cd seq_dict
-    picard CreateSequenceDictionary R=$base O="${fasta.baseName}.dict"
+    picard -Xmx${task.memory.toMega()}M -Xms${task.memory.toMega()}M CreateSequenceDictionary R=$base O="${fasta.baseName}.dict"
     """
 }
 
@@ -970,7 +970,7 @@ process markDup{
     script:
     prefix = "${bam.baseName}"
     """
-    picard MarkDuplicates INPUT=$bam OUTPUT=${prefix}.markDup.bam REMOVE_DUPLICATES=TRUE AS=TRUE METRICS_FILE="${prefix}.markdup.metrics" VALIDATION_STRINGENCY=SILENT
+    picard -Xmx${task.memory.toMega()}M -Xms${task.memory.toMega()}M MarkDuplicates INPUT=$bam OUTPUT=${prefix}.markDup.bam REMOVE_DUPLICATES=TRUE AS=TRUE METRICS_FILE="${prefix}.markdup.metrics" VALIDATION_STRINGENCY=SILENT
     """
 }